diversity.stats-methods: Diversities

Description Usage Arguments Details Value References Examples

Description

A generic function to calculate nucleotide & haplotype diversities.

Usage

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## S4 method for signature 'GENOME'
diversity.stats(object,new.populations=FALSE,subsites=FALSE,pi=FALSE, keep.site.info=TRUE)

Arguments

object

An object of class "GENOME"

new.populations

list of populations. default=FALSE

subsites

"transitions": SNPs that are transitions.
"transversions": SNPs that are transversions.
"syn": synonymous sites.
"nonsyn": nonsynonymous sites.
"exon": SNPs in exon regions.
"intron": SNPs in intron regions.
"coding": SNPs in coding regions (CDS).
"utr": SNPs in UTR regions.
"gene": SNPs in genes.
"intergenic" : SNPs in intergenic regions.

pi

Nei's calculation of pi

keep.site.info

stores site specific values in [email protected]

Details

The nucleotide diversities have to be devided by [email protected] to give diversities per site.

Value

Returned value is a modified object of class "GENOME"

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The following slots will be modified in the "GENOME" object
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Slot Reference Description
1. nuc.diversity.within [1,3] Nucleotide diversity (within the population)
2. Pi [2] Diversity from Nei (within the population)
3. hap.diversity.within [1] Haplotype diversity (within the population)

References

[1] Hudson, R. R., M. Slatkin, and W.P. Maddison (1992). Estimating of levels of gene flow from DNA sequence data. Gentics 13(2),583-589

[2] Nei, M. (1987). Molecular Evolutionary Genetics. Columbia Univ. Press, New York.

[3] Wakeley, J. (1996).The Variance of Pairwise Nucleotide Differences in Two Populations with Migration. THEORETICAL POPULATION BIOLOGY. 49, 39-57.

Examples

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# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- diversity.stats(GENOME.class)
# GENOME.class <- diversity.stats(GENOME.class,list(1:4,5:10))
# GENOME.class <- diversity.stats(GENOME.class,
# list(c("seq1","seq5","seq3"),c("seq2","seq8")))
# show the result:
# [email protected]

pievos101/PopGenome documentation built on May 16, 2019, 2:54 a.m.